Fig. 4: Hub architecture of the ssDNA-27_+8ds+9_+143-R fully assembled relaxosome structure and overview of hub 1.
Proteins and DNAs are shown in ribbon representation. Secondary structures involved in DNA-binding are labelled. In panels b, c insets of the entire structure are provided for orientation. Within insets, dash-lined box shows the region(s) detailed in the corresponding panel(s). a Hub definition. The 4 hubs are shown within dotted lined ovals (except for hub 4) and are labelled hub1-4. b Hub1. Top: IHF-DNA interaction. Interactions are dominated by residues in the β2-5 region with bending triggered by insertion of the β2−3 hairpin into the major groove of the DNA (see Supplementary Fig. 7a, top panel, for details). Bottom: protein-protein interactions between TraY1, IHF and TraI VH2A+2B/2B-like (see Supplementary Fig. 7a, bottom panel for details). TraY1 has a 12 residue N-terminal tail, the very N-terminus of which is involved in interaction with residues in α1 and the α1-α2 loop of IHFα. The remaining N-terminal tail residues as well as many residues in its α3 helix interact with TraI VH. In TraI VH, residues in αM and the β9-αM and β11-β12 loops are implicated in TraY1 binding while other residues in β12, β13 and in the β11-β12 loop interact with residues in α2 and the α1-α2 loop of both IHFα and β. (see Supplementary Fig. 7a for details). c Interactions between TraI VH2A+2B/2B-like and DNA. Two regions of TraI VH are responsible for dsDNA binding at oriT: the tip of the 2B-like domain and a region of the 2A domain (details in Supplementary Fig. 7b). VH2B/2B-like also forms a three-way interaction in all complexes described here with IHF and TraY1 in hub 1, while also interacting with the TE domain of TraI in the ss-27_+8ds+9_+143-R complex in hub 3.
